Professional Details

Work Experience: Postdoc, POSTECH, South Korea Postdoc, Max-Planck-Institute for Coal Research, Germany, Postdoc, University of Duisburg-Essen, Germany Visiting Scientist, Queen Mary University of London, London, England Assistant Professor, Chettinad Hospital and Research Institute, India

Orcid ID: 0000-0002-6692-7066

Examinership: Internal examiner for M.Sc. Medical Biotechnology

Contact Details

Phone number: 7708758510

Email Official:

Email Personal: pandian.sokkar@gmail.com

Research – Major Research Areas

  • Computational Chemistry, biomolecular simulation, drug design

Research – Clinical Trials / Funded Projects

  • DST SERB SRG 2019

Research – List of Publications

  • Johannes Knorr, Pandian Sokkar, Paolo Costa, Wolfram Sander, Elsa Sanchez-Garcia and Patrick Nuernberger. “”How protic solvents determine the reaction mechanisms of diphenylcarbene in solution”. Journal of Organic Chemistry (2019) In press.
  • Nadja Berger, Laura Wollny, Pandian Sokkar,Elsa Sanchez-Garcia. “Solvent Enhanced Conformational Flexibility of Cyclic Tetrapeptides”. ChemPhysChem (2019) 20:1664-1670.
  • Frank Schulz, Michael Dirkmann, Javier Iglesias, Victor Muñoz, Pandian Sokkar,  Elsa Sanchez-Garcia. “A multi-perspective approach to solvent regulation of enzymatic activity: HMG-CoA reductase”. ChemBioChem (2018) 19:153–158
  • Banafshe Zakeri, Stephan Niebling, Alba Gigante Martinez, Pandian Sokkar, Elsa Sanchez Garcia, Carsten Schmuck, Sebastian Schluc̈ ker. “Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy”. Physical Chemistry Chemical Physics (2018) 20:1817-1820
  • Nils Schulz, Pandian Sokkar, Elric Engelage, Severin Schindler, Mate Erdelyi, Elsa Sanchez- Garcia, Stefan Matthias Huber. “The Interaction Modes of Haloimidazolium Salts in Solution”. Chemistry-A European Journal (2017) 23:1–11
    Page 2 of 3
  • Johannes Knorr, Pandian Sokkar, Sebastian Schott, Paolo Costa, Walter Thiel, Wolfram Sander, Elsa Sanchez-Garcia, Patrick Nuernberger. “”Competitive solvent-molecule interactions govern primary processes of diphenylcarbene in solvent mixtures”. Nature communications (2016) 7:12968
  • Stefan Henkel, Paolo Costa, Linda Klute, Pandian Sokkar, Miguel Fernandez-Oliva, Walter Thiel, Elsa Sanchez-Garcia, Wolfram Sander. “”Switching the spin state of diphenylcarbene via halogen bonding”. Journal of American Chemical Society (2016) 138:1689-1697
  • Pandian Sokkar, Eliot Boulanger, Walter Thiel, Elsa Sanchez-Garcia. “Hybrid quantum mechanics/molecular mechanics/coarse-grained modeling: a triple-resolution approach for biomolecular systems”. Journal of chemical theory and computation (2015) 11:1809–1818
  • Namgung Ran, Yeong Mi Lee, Jihoon Kim, Yuna Jang, Byung-Heon Lee, Pandian Sokkar, Young Min Rhee, Allan S. Hoffman, Won Jong Kim. “”Poly-cyclodextrin and poly-paclitaxel nano-assembly for anticancer therapy”. Nature communications (2014) 5:3702
  • Pandian Sokkar, Sun-Mi Choi, Young Min Rhee. “Simple method for simulating the mixture of atomistic and coarse-grained molecular systems”. Journal of chemical theory and computation (2013) 9:3728−3739
  • Stephen Michael Rajesh, Subbu Perumal, J. Carlos Menéndez, Sokkar Pandian, Ramachandran Murugesan. “Facile ionic liquid-mediated, three-component sequential reactions for the green, regio- and diastereoselective synthesis of furocoumarins”. Tetrahedron (2012) 68:5631-5636
  • Pandian Sokkar, Vani Sathis, Murugesan Ramachandran. “Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies”. Journal of Molecular Modeling (2012) 18:1691-1700
  • Pandian Sokkar, Shylajanaciyar Mohandass, Murugesan Ramachandran. “Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking”. Journal of Molecular Modeling (2011) 17:1565–1577
  • Toshihide Yamasaki, Fumiya Mito, Yuko Ito, Sokkar Pandian, Yuichi Kinoshita, Koji Nakano, Ramachandran Murugesan, Kiyoshi Sakai, Hideo Utsumi, Ken-ichi Yamada. “Structure- Reactivity Relationship of Piperidine Nitroxide: Electrochemical, ESR and Computational Studies”. Journal of Organic Chemistry (2011) 76:435–440
  • Sai Shyam Narayanan, Pandian Sokkar, Murugesan Ramachandran, Kesavan Madhavan Nampoothiri. “Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis”. FEMS Microbiology Letters (2011) 320:40-47
  • Y. Yesuthangam, S. Pandian, K Venkatesan, R Gandhidasan, R Murugesan. “Photogeneration of reactive oxygen species and photoinduced plasmid DNA cleavage by novel synthetic chalcones”. Journal of Photochemistry and Photobiology B (2010) 102:200–208″

Reviewer for Scientific Journals / Research Proposals

  • Carbohydrate Polymers, Process of Biochemistry, Applied Biochemistry and Biotechnology
  • “Journal of Molecular Modeling, Plos ONE”

Research Topics

  • “Biomolecular simulation: Classical MD simulation approaches to investigate important biomolecules/drug targets (GPCR, enzymes, ribosome, etc.)
  • Protein-ligand/protein-peptide interaction: MD simulation, free energy calculations, pulling simulations, docking, lead optimization
  • Nanoparticle simulation: Coarse-Grained (CG) MD simulation of mesoscopic systems (such as polymer-based nanoparticles) to assess the thermal stability
  • Hybrid multi-resolution approaches: Method development and application of multi-resolution models (QM/MM, atomistic/CG models) for biological and drug design applications
  • Reaction mechanism: Investigation of reaction mechanisms in enzymes or insolvent media by QM/MM methods (MDs, reaction coordinate optimization)”
  • 3 Presented
  • 7 posters

Major Awards/Honours and Fellowships

  • UGC-NET/JRF
Research and Publication

Research – Major Research Areas

  • Computational Chemistry, biomolecular simulation, drug design

Research – Clinical Trials / Funded Projects

  • DST SERB SRG 2019

Research – List of Publications

  • Johannes Knorr, Pandian Sokkar, Paolo Costa, Wolfram Sander, Elsa Sanchez-Garcia and Patrick Nuernberger. “”How protic solvents determine the reaction mechanisms of diphenylcarbene in solution”. Journal of Organic Chemistry (2019) In press.
  • Nadja Berger, Laura Wollny, Pandian Sokkar,Elsa Sanchez-Garcia. “Solvent Enhanced Conformational Flexibility of Cyclic Tetrapeptides”. ChemPhysChem (2019) 20:1664-1670.
  • Frank Schulz, Michael Dirkmann, Javier Iglesias, Victor Muñoz, Pandian Sokkar,  Elsa Sanchez-Garcia. “A multi-perspective approach to solvent regulation of enzymatic activity: HMG-CoA reductase”. ChemBioChem (2018) 19:153–158
  • Banafshe Zakeri, Stephan Niebling, Alba Gigante Martinez, Pandian Sokkar, Elsa Sanchez Garcia, Carsten Schmuck, Sebastian Schluc̈ ker. “Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy”. Physical Chemistry Chemical Physics (2018) 20:1817-1820
  • Nils Schulz, Pandian Sokkar, Elric Engelage, Severin Schindler, Mate Erdelyi, Elsa Sanchez- Garcia, Stefan Matthias Huber. “The Interaction Modes of Haloimidazolium Salts in Solution”. Chemistry-A European Journal (2017) 23:1–11
    Page 2 of 3
  • Johannes Knorr, Pandian Sokkar, Sebastian Schott, Paolo Costa, Walter Thiel, Wolfram Sander, Elsa Sanchez-Garcia, Patrick Nuernberger. “”Competitive solvent-molecule interactions govern primary processes of diphenylcarbene in solvent mixtures”. Nature communications (2016) 7:12968
  • Stefan Henkel, Paolo Costa, Linda Klute, Pandian Sokkar, Miguel Fernandez-Oliva, Walter Thiel, Elsa Sanchez-Garcia, Wolfram Sander. “”Switching the spin state of diphenylcarbene via halogen bonding”. Journal of American Chemical Society (2016) 138:1689-1697
  • Pandian Sokkar, Eliot Boulanger, Walter Thiel, Elsa Sanchez-Garcia. “Hybrid quantum mechanics/molecular mechanics/coarse-grained modeling: a triple-resolution approach for biomolecular systems”. Journal of chemical theory and computation (2015) 11:1809–1818
  • Namgung Ran, Yeong Mi Lee, Jihoon Kim, Yuna Jang, Byung-Heon Lee, Pandian Sokkar, Young Min Rhee, Allan S. Hoffman, Won Jong Kim. “”Poly-cyclodextrin and poly-paclitaxel nano-assembly for anticancer therapy”. Nature communications (2014) 5:3702
  • Pandian Sokkar, Sun-Mi Choi, Young Min Rhee. “Simple method for simulating the mixture of atomistic and coarse-grained molecular systems”. Journal of chemical theory and computation (2013) 9:3728−3739
  • Stephen Michael Rajesh, Subbu Perumal, J. Carlos Menéndez, Sokkar Pandian, Ramachandran Murugesan. “Facile ionic liquid-mediated, three-component sequential reactions for the green, regio- and diastereoselective synthesis of furocoumarins”. Tetrahedron (2012) 68:5631-5636
  • Pandian Sokkar, Vani Sathis, Murugesan Ramachandran. “Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies”. Journal of Molecular Modeling (2012) 18:1691-1700
  • Pandian Sokkar, Shylajanaciyar Mohandass, Murugesan Ramachandran. “Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking”. Journal of Molecular Modeling (2011) 17:1565–1577
  • Toshihide Yamasaki, Fumiya Mito, Yuko Ito, Sokkar Pandian, Yuichi Kinoshita, Koji Nakano, Ramachandran Murugesan, Kiyoshi Sakai, Hideo Utsumi, Ken-ichi Yamada. “Structure- Reactivity Relationship of Piperidine Nitroxide: Electrochemical, ESR and Computational Studies”. Journal of Organic Chemistry (2011) 76:435–440
  • Sai Shyam Narayanan, Pandian Sokkar, Murugesan Ramachandran, Kesavan Madhavan Nampoothiri. “Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis”. FEMS Microbiology Letters (2011) 320:40-47
  • Y. Yesuthangam, S. Pandian, K Venkatesan, R Gandhidasan, R Murugesan. “Photogeneration of reactive oxygen species and photoinduced plasmid DNA cleavage by novel synthetic chalcones”. Journal of Photochemistry and Photobiology B (2010) 102:200–208″

Reviewer for Scientific Journals / Research Proposals

  • Carbohydrate Polymers, Process of Biochemistry, Applied Biochemistry and Biotechnology
  • “Journal of Molecular Modeling, Plos ONE”

Research Topics

  • “Biomolecular simulation: Classical MD simulation approaches to investigate important biomolecules/drug targets (GPCR, enzymes, ribosome, etc.)
  • Protein-ligand/protein-peptide interaction: MD simulation, free energy calculations, pulling simulations, docking, lead optimization
  • Nanoparticle simulation: Coarse-Grained (CG) MD simulation of mesoscopic systems (such as polymer-based nanoparticles) to assess the thermal stability
  • Hybrid multi-resolution approaches: Method development and application of multi-resolution models (QM/MM, atomistic/CG models) for biological and drug design applications
  • Reaction mechanism: Investigation of reaction mechanisms in enzymes or insolvent media by QM/MM methods (MDs, reaction coordinate optimization)”
Conferences - Papers presented
Awards, Achievements & Fellowships

© 2020 Chettinad Academy